fix(setup): preserve registration identity and recovery ownership

Keep layered environment choices, current byte-exact recovery snapshots, and package-manager failure details. Report pinned package drift without claiming runner resolution. Retain failed Linux installer cleanup for host-owned retry while preserving the install outcome.

Reviewed fixes include #2632, #2769, #2783, #2959, #2979, #2983, #2995, #3009, and #2559.

Validation: 98 focused setup/registration tests passed; 45 Linux installer tests passed. Real Linux package installation remains unverified.

src/application/ClientConfigurationFiles.ts

@@ -11,6 +11,21 @@ import {
 import type { SetupClient } from "./SupportedClients.js";
 import { clientRegistrationEnvironment } from "./ClientRegistrationEnvironment.js";
 import type { ArtifactResourceScope } from "../artifacts/ArtifactResourceScope.js";
+import type { ConfigurationError } from "../domain/configurationErrors.js";
+
+/** A parsed layer retains its path so rereading the write target replaces only that layer. */
+export interface ClientConfigurationSource extends ClientConfigurationDocument {
+  readonly sourcePath: string;
+}
+
+const invalidEnvironment = (
+  path: string,
+  error: ConfigurationError,
+): ClientConfigurationFileError => ({
+  kind: "malformed",
+  path,
+  detail: `Configuration ${path} has an invalid REA server environment: ${error.settings.map(({ setting, constraint }) => `${setting}: ${constraint}`).join("; ")}. Repair it before rerunning setup.`,
+});
 
 /** A named source failure that setup can explain without losing the bad path. */
 export interface ClientConfigurationFileError {
@@ -74,9 +89,9 @@ export const readClientConfigurationFiles = async (
   client: SetupClient,
   resources?: ArtifactResourceScope,
 ): Promise<
-  Result<readonly ClientConfigurationDocument[], ClientConfigurationFileError>
+  Result<readonly ClientConfigurationSource[], ClientConfigurationFileError>
 > => {
-  const documents: ClientConfigurationDocument[] = [];
+  const documents: ClientConfigurationSource[] = [];
   for (const path of client.configPaths ?? [client.configPath]) {
     const document = await readConfigurationFile(
       path,
@@ -85,16 +100,21 @@ export const readClientConfigurationFiles = async (
     );
     if (!document.ok) return document;
     if (document.value !== undefined) {
-      const environment = clientRegistrationEnvironment(document.value);
+      const environment = clientRegistrationEnvironment(
+        document.value,
+        {},
+        "fragment",
+      );
       if (!environment.ok)
-        return err({
-          kind: "malformed",
-          path,
-          detail: `Configuration ${path} has an invalid REA server environment: ${environment.error.settings.map(({ setting, constraint }) => `${setting}: ${constraint}`).join("; ")}. Repair it before rerunning setup.`,
-        });
-      documents.push(document.value);
+        return err(invalidEnvironment(path, environment.error));
+      documents.push({ ...document.value, sourcePath: path });
     }
   }
+  const environment = clientRegistrationEnvironment(
+    effectiveClientConfiguration(documents),
+  );
+  if (!environment.ok)
+    return err(invalidEnvironment(client.configPath, environment.error));
   return ok(documents);
 };
 
@@ -117,8 +137,24 @@ const isObject = (value: unknown): value is Record<string, unknown> =>
 
 /** Project a client's effective user registration without modifying its source files. */
 export const effectiveClientConfiguration = (
-  documents: readonly ClientConfigurationDocument[],
+  sources: readonly ClientConfigurationSource[],
+  target?: {
+    readonly client: Pick<SetupClient, "configPath" | "configPaths">;
+    readonly document: ClientConfigurationDocument | undefined;
+  },
 ): ClientConfigurationDocument | undefined => {
+  const documents =
+    target === undefined
+      ? sources
+      : (target.client.configPaths ?? [target.client.configPath]).flatMap(
+          (path) => {
+            const document =
+              path === target.client.configPath
+                ? target.document
+                : sources.find(({ sourcePath }) => sourcePath === path);
+            return document === undefined ? [] : [document];
+          },
+        );
   const last = documents.at(-1);
   if (last === undefined) return undefined;
   if (documents.length === 1) return last;